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How to manage changes in maps?

Hi to all, it's my first post here.
I've been around for a while and this is great community.
I'd like to get some advices from you, much more experienced cartographers than me.
I am writing a fantasy book with (of course!) a map, and maybe some more maps for different historical periods.
I started with some scratch maps but soon i realized that (especially when my book is read by other ppl) i need quite polished maps to enjoy reading, correcting, and progressing the story itself, because the map is very important and is a consistent part of the (imaginary) world.
Here comes my problem: how can i manage changes in map?
I am using Inkscape because i do not like non-scaling images.
At the moment i am using different layers for:

Background (map "paper")

Coastal line

Mountains, forests and other environmental elements

Rivers / lakes

Big cities

Little cities

Cities names

Geographical names

"Rendering" layers (fog, grass, snow...)

When i need to do some changes in a city name or in the shape of a lake, or i need to put a new lake, my method is ok.
But if i need a new region, or i decide that a kingdom of the map has no sense anymore and i want to delete it, the change affects heavily all layers.
I thought that i could make a layer for each region, with (sub)layers in them...but this means a *lot* of layers (5-10 regions x 5-10 layers... 25-100 layers!) or should i do a different file for each region and assemble them after printing?
What methods do you use to manage this kind of things?
It seems that the problem is even bigger with non-svg softwares, and this is the second reason for which i am using inkscape. Managing a changing and half-finished map in a traditional software as far as i know is almost impossibile, but maybe i am wrong.

hi d3ko, congrats on your step up from lurker into the hallowed halls of the cartographer
There is no easy way to do what you propose, because removing a whole region from a map will of course leave a giant hole which then makes it necessary to move borders and so forth. So that would affect not only the deleted region but all regions on the map. If you put your borders in a layer of its own, you can just adjust in that layer - but naming convention for cities and lakes might be different from region to region and the new borders might change a lot of names also.
Working with many layers however is very normal for digital artists, I seldom end up with less than 50 in photoshop and often more than 100 - and in Illustrator counting sublayers and every object gets its own layer there will be thousands of layers. So the only problem there can be the capacity of the computer in question.

Thank you for your reply
Maybe i could try to work with more layers, usually i try to keep the # of layers low... but if you say it's usual to work with 100 layers, i will try
It could be a viable solution, i think...
What you say about naming convention is true, and moreover the font often is different. Separating layers for different names in regions it's a good idea.
I will check your method, considering that if i put each region on its own layer i can even *move* it, thing that is impossible the way i am working now. It's not so crazy to "move" a region because there are some elements that are movable (lakes, islands, group of islands, and so on...).
It could be also a good idea to give regions a different colour (even if lightly coloured) instead of a border, at least for the "work in progress".
This could be more manageable than "classic" borders... and i could remove them later, still having a visually good map in the meanwhile...
(sorry for my english, but i realized that it's not so easy to speak of arguments that are new to me... my english comes from IT environments and the terms are quite different!)
Thank you

You can have a look at my sig with my ViewingDale app. It does not have a traditional method of doing maps that would allow you to do these changes more easily. The app works by using bitmaps but these are scalable. You use them like a stamp tool that is to say you put a lot of images down on top of one another. Its like a gigantic composite of them. Each item (parent) has multiple child images attached so that you would have all the images for one region together. You can then move the entire region in one go. Since its not merged at any point it does not ever have a point that you cannot undo which is unlike inkscape or paint packages. The app is more of a universe or campaign manager via a map than a strict mapping app tho so you still need to create the images in isolation using inkscape or a paint package but it would handle the composition of them in a way that solves your problem.